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Chang C, Zhang H, Lu J, Si H, Ma C. Genetic Improvement of Wheat with Pre-Harvest Sprouting Resistance in China. Genes (Basel) 2023; 14:genes14040837. [PMID: 37107595 PMCID: PMC10137347 DOI: 10.3390/genes14040837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Wheat pre-harvest sprouting (PHS) refers to the germination of seeds directly on the spike due to rainy weather before harvest, which often results in yield reduction, quality deterioration, and seed value loss. In this study, we reviewed the research progress in the quantitative trait loci (QTL) detection and gene excavation related to PHS resistance in wheat. Simultaneously, the identification and creation of germplasm resources and the breeding of wheat with PHS resistance were expounded in this study. Furthermore, we also discussed the prospect of molecular breeding during genetic improvement of PHS-resistant wheat.
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Kumar M, Kumar S, Sandhu KS, Kumar N, Saripalli G, Prakash R, Nambardar A, Sharma H, Gautam T, Balyan HS, Gupta PK. GWAS and genomic prediction for pre-harvest sprouting tolerance involving sprouting score and two other related traits in spring wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:14. [PMID: 37313293 PMCID: PMC10248620 DOI: 10.1007/s11032-023-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 01/26/2023] [Indexed: 06/15/2023]
Abstract
In wheat, a genome-wide association study (GWAS) and genomic prediction (GP) analysis were conducted for pre-harvest sprouting (PHS) tolerance and two of its related traits. For this purpose, an association panel of 190 accessions was phenotyped for PHS (using sprouting score), falling number, and grain color over two years and genotyped with 9904 DArTseq based SNP markers. GWAS for main-effect quantitative trait nucleotides (M-QTNs) using three different models (CMLM, SUPER, and FarmCPU) and epistatic QTNs (E-QTNs) using PLINK were performed. A total of 171 M-QTNs (CMLM, 47; SUPER, 70; FarmCPU, 54) for all three traits, and 15 E-QTNs involved in 20 first-order epistatic interactions were identified. Some of the above QTNs overlapped the previously reported QTLs, MTAs, and cloned genes, allowing delineating 26 PHS-responsive genomic regions that spread over 16 wheat chromosomes. As many as 20 definitive and stable QTNs were considered important for use in marker-assisted recurrent selection (MARS). The gene, TaPHS1, for PHS tolerance (PHST) associated with one of the QTNs was also validated using the KASP assay. Some of the M-QTNs were shown to have a key role in the abscisic acid pathway involved in PHST. Genomic prediction accuracies (based on the cross-validation approach) using three different models ranged from 0.41 to 0.55, which are comparable to the results of previous studies. In summary, the results of the present study improved our understanding of the genetic architecture of PHST and its related traits in wheat and provided novel genomic resources for wheat breeding based on MARS and GP. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01357-5.
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Affiliation(s)
- Manoj Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | | | - Neeraj Kumar
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC USA
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD USA
| | - Ram Prakash
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Akash Nambardar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Hemant Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
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Rabieyan E, Bihamta MR, Moghaddam ME, Mohammadi V, Alipour H. Genome-wide association mapping and genomic prediction for pre‑harvest sprouting resistance, low α-amylase and seed color in Iranian bread wheat. BMC PLANT BIOLOGY 2022; 22:300. [PMID: 35715737 PMCID: PMC9204952 DOI: 10.1186/s12870-022-03628-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pre-harvest sprouting (PHS) refers to a phenomenon, in which the physiologically mature seeds are germinated on the spike before or during the harvesting practice owing to high humidity or prolonged period of rainfall. Pre-harvest sprouting (PHS) remarkably decreases seed quality and yield in wheat; hence it is imperative to uncover genomic regions responsible for PHS tolerance to be used in wheat breeding. A genome-wide association study (GWAS) was carried out using 298 bread wheat landraces and varieties from Iran to dissect the genomic regions of PHS tolerance in a well-irrigated environment. Three different approaches (RRBLUP, GBLUP and BRR) were followed to estimate prediction accuracies in wheat genomic selection. RESULTS Genomes B, A, and D harbored the largest number of significant marker pairs (MPs) in both landraces (427,017, 328,006, 92,702 MPs) and varieties (370,359, 266,708, 63,924 MPs), respectively. However, the LD levels were found the opposite, i.e., genomes D, A, and B have the highest LD, respectively. Association mapping by using GLM and MLM models resulted in 572 and 598 marker-trait associations (MTAs) for imputed SNPs (- log10 P > 3), respectively. Gene ontology exhibited that the pleitropic MPs located on 1A control seed color, α-Amy activity, and PHS. RRBLUP model indicated genetic effects better than GBLUP and BRR, offering a favorable tool for wheat genomic selection. CONCLUSIONS Gene ontology exhibited that the pleitropic MPs located on 1A can control seed color, α-Amy activity, and PHS. The verified markers in the current work can provide an opportunity to clone the underlying QTLs/genes, fine mapping, and genome-assisted selection.Our observations uncovered key MTAs related to seed color, α-Amy activity, and PHS that can be exploited in the genome-mediated development of novel varieties in wheat.
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Affiliation(s)
- Ehsan Rabieyan
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Mohammad Reza Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | | | - Valiollah Mohammadi
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
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Gautam T, Kumar K, Agarwal P, Tyagi S, Jaiswal V, Gahlaut V, Kumar S, Prasad P, Chhuneja P, Balyan HS, Gupta PK. Development of white-grained PHS-tolerant wheats with high grain protein and leaf rust resistance. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:42. [PMID: 37309440 PMCID: PMC10236099 DOI: 10.1007/s11032-021-01234-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/17/2021] [Indexed: 06/14/2023]
Abstract
The present study involved incorporation of two major QTLs for pre-harvest sprouting tolerance (PHST) in an Indian wheat cultivar named Lok1, which happens to be PHS susceptible. For transfer of two QTLs, two independent programmes with two different donors (AUS1408, CN19055) were utilized. The recipient cv. Lok1 was crossed with each of the two donors, followed by a number of backcrosses. Each backcross progeny was subjected to foreground and background selections. KASP assay was also used for confirming the presence of PHST QTL. In one case, PHST QTL was later also pyramided with a gene for high grain protein content (Gpc-B1) and a gene for leaf rust resistance (Lr24). The MAS derived lines were screened for PHS using simulated rain chambers leading to selection of 10 PHST lines. Four of these advanced lines carried all the three QTL/genes and exhibited high level of PHST (PHS score 2-3) associated with significant improvement in GPC and resistance against leaf rust. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01234-z.
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Affiliation(s)
- Tinku Gautam
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, UP 250004 India
| | - Kuldeep Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, UP 250004 India
| | - Priyanka Agarwal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, UP 250004 India
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Sandhya Tyagi
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, UP 250004 India
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Vandana Jaiswal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, UP 250004 India
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061 India
| | - Vijay Gahlaut
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, UP 250004 India
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061 India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, UP 250004 India
| | - Pramod Prasad
- Regional Station, ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002 India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141027 India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, UP 250004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, UP 250004 India
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Identification of a major-effect QTL associated with pre-harvest sprouting in cucumber (Cucumis sativus L.) using the QTL-seq method. BMC Genomics 2021; 22:249. [PMID: 33827431 PMCID: PMC8028694 DOI: 10.1186/s12864-021-07548-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/17/2021] [Indexed: 11/13/2022] Open
Abstract
Background Cucumber (Cucumis sativus L.) is cultivated worldwide, and it is essential to produce enough high-quality seeds to meet demand. Pre-harvest sprouting (PHS) in cucumber is a critical problem and causes serious damage to seed production and quality. Nevertheless, the genetic basis and molecular mechanisms underlying cucumber PHS remain unclear. QTL-seq is an efficient approach for rapid quantitative trait loci (QTL) identification that simultaneously takes advantage of bulked-segregant analysis (BSA) and whole-genome resequencing. In the present research, QTL-seq analysis was performed to identify QTLs associated with PHS in cucumber using an F2 segregating population. Results Two QTLs that spanned 7.3 Mb on Chromosome 4 and 0.15 Mb on Chromosome 5 were identified by QTL-seq and named qPHS4.1 and qPHS5.1, respectively. Subsequently, SNP and InDel markers selected from the candidate regions were used to refine the intervals using the extended F2 populations grown in the 2016 and 2017 seasons. Finally, qPHS4.1 was narrowed to 0.53 Mb on chromosome 4 flanked by the markers SNP-16 and SNP-24 and was found to explain 19–22% of the phenotypic variation in cucumber PHS. These results reveal that qPHS4.1 is a major-effect QTL associated with PHS in cucumber. Based on gene annotations and qRT-PCR expression analyses, Csa4G622760 and Csa4G622800 were proposed as the candidate genes. Conclusions These results provide novel insights into the genetic mechanism controlling PHS in cucumber and highlight the potential for marker-assisted selection of PHS resistance breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07548-8.
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Identification of QTLs and a Candidate Gene for Reducing Pre-Harvest Sprouting in Aegilops tauschii- Triticum aestivum Chromosome Segment Substitution Lines. Int J Mol Sci 2021; 22:ijms22073729. [PMID: 33918469 PMCID: PMC8038248 DOI: 10.3390/ijms22073729] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/03/2022] Open
Abstract
Wheat pre-harvest sprouting (PHS) causes serious losses in wheat yield. In this study, precise mapping was carried out in the chromosome segment substitution lines (CSSL) F2 population generated by a direct cross of Zhoumai 18 (PHS-sensitive) and Aegilops tauschii accession T093 (highly PHS-resistant). Three Ae. tauschii-derived quantitative trait loci (QTLs), QDor.3D.1, QDor.3D.2, and QDor.3D.3, were detected on chromosome 3DL using four simple sequence repeats (SSR) markers and 10 developed Kompetitive allele-specific PCR (KASP) markers. Alongside these QTL results, the RNA-Seq and qRT-PCR analysis revealed expression levels of TraesCS3D01G466100 in the QDor.3D.2 region that were significantly higher in CSSLs 495 than in Zhoumai 18 during the seed imbibition treatment. The cDNA sequencing results of TraesCS3D01G466100 showed two single nucleotide polymorphisms (SNPs), resulting in two changed amino acid substitutions between Zhoumai 18 and line 495, and the 148 nt amino acid substitution of TraesCS3D01G466100, derived from Ae. tauschii T093, which may play an important role in the functioning of ubiquitin ligase enzymes 3 (E3) according to the homology protein analysis, which could lead to differential PHS-resistance phenotypes. Taken together, our results may foster a better understanding of the mechanism of PHS resistance and are potentially valuable for marker-assisted selection in practical wheat breeding efforts.
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Li L, Zhang Y, Zhang Y, Li M, Xu D, Tian X, Song J, Luo X, Xie L, Wang D, He Z, Xia X, Zhang Y, Cao S. Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays. FRONTIERS IN PLANT SCIENCE 2021; 12:749206. [PMID: 34721477 PMCID: PMC8551680 DOI: 10.3389/fpls.2021.749206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/13/2021] [Indexed: 05/13/2023]
Abstract
Preharvest sprouting (PHS) significantly reduces grain yield and quality. Identification of genetic loci for PHS resistance will facilitate breeding sprouting-resistant wheat cultivars. In this study, we constructed a genetic map comprising 1,702 non-redundant markers in a recombinant inbred line (RIL) population derived from cross Yangxiaomai/Zhongyou9507 using the wheat 15K single-nucleotide polymorphism (SNP) assay. Four quantitative trait loci (QTL) for germination index (GI), a major indicator of PHS, were identified, explaining 4.6-18.5% of the phenotypic variances. Resistance alleles of Qphs.caas-3AL, Qphs.caas-3DL, and Qphs.caas-7BL were from Yangxiaomai, and Zhongyou9507 contributed a resistance allele in Qphs.caas-4AL. No epistatic effects were detected among the QTL, and combined resistance alleles significantly increased PHS resistance. Sequencing and linkage mapping showed that Qphs.caas-3AL and Qphs.caas-3DL corresponded to grain color genes Tamyb10-A and Tamyb10-D, respectively, whereas Qphs.caas-4AL and Qphs.caas-7BL were probably new QTL for PHS. We further developed cost-effective, high-throughput kompetitive allele-specific PCR (KASP) markers tightly linked to Qphs.caas-4AL and Qphs.caas-7BL and validated their association with GI in a test panel of cultivars. The resistance alleles at the Qphs.caas-4AL and Qphs.caas-7BL loci were present in 72.2 and 16.5% cultivars, respectively, suggesting that the former might be subjected to positive selection in wheat breeding. The findings provide not only genetic resources for PHS resistance but also breeding tools for marker-assisted selection.
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Affiliation(s)
- Lingli Li
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingjun Zhang
- Hebei Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yong Zhang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ming Li
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengan Xu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Xiuling Tian
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Song
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xumei Luo
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lina Xie
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Desen Wang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Beijing, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Zhang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
- Yan Zhang
| | - Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Shuanghe Cao
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Liu S, Wang D, Lin M, Sehgal SK, Dong L, Wu Y, Bai G. Artificial selection in breeding extensively enriched a functional allelic variation in TaPHS1 for pre-harvest sprouting resistance in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:339-350. [PMID: 33068119 DOI: 10.1007/s00122-020-03700-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
Pre-harvest sprouting (PHS) causes significant losses in wheat yield and quality worldwide. Previously, we cloned a PHS resistance gene, TaPHS1, and identified two causal mutations for reduced seed dormancy (SD) and increased PHS susceptibility. Here we identified a novel allelic variation of C to T transition in 3'-UTR of TaPHS1, which associated with reduced SD and PHS resistance. The T allele occurred in wild wheat progenitors and was likely the earliest functional mutation in TaPHS1 for PHS susceptibility. Allele frequency analysis revealed low frequency of the T allele in wild diploid and tetraploid wheat progenitors, but very high frequency in modern wheat cultivars and breeding lines, indicating that artificial selection quickly enriched the T allele during modern breeding. The T allele was significantly associated with short SD in both T. aestivum and T. durum, the two most cultivated species of wheat. This variation together with previously reported functional sequence variations co-regulated TaPHS1 expression levels and PHS resistance in different germplasms. Haplotype analysis of the four functional variations identified the best PHS resistance haplotype of TaPHS1. The resistance haplotype can be used in marker-assisted selection to transfer TaPHS1 to new wheat cultivars.
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Affiliation(s)
- Shubing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Danfeng Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Meng Lin
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Lei Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yuye Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
- USDA-ARS, Hard Winter Wheat Genetic Research Unit, Manhattan, KS, 66506, USA.
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Liton MMUA, McCartney CA, Hiebert CW, Kumar S, Jordan MC, Ayele BT. Identification of loci for pre-harvest sprouting resistance in the highly dormant spring wheat RL4137. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:113-124. [PMID: 33001261 DOI: 10.1007/s00122-020-03685-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/11/2020] [Indexed: 05/06/2023]
Abstract
Combination of RL4137 alleles at three QTLs on chromosomes 4A, 6B and 6D, and 'Roblin' allele at a novel QTL on chromosome 1D increases pre-harvest sprouting resistance in 'Roblin'/RL4137 doubled haploid population. Pre-harvest sprouting (PHS) significantly reduces wheat grain yield and quality. Therefore, identifying quantitative trait loci (QTL) for PHS resistance is key to facilitate marker-assisted breeding. To this end, we studied PHS in a population of 330 doubled haploid (DH) lines derived from 'Roblin'/RL4137. The parental and DH lines were examined for their PHS phenotype based on speed of germination index in five environments and genotyped using the wheat Infinium 90 K SNP array. A total of five QTLs were detected on linkage groups 1D, 4A.2, 6B.1, 6D and 7A over the five environments. The QTL QPhs.umb-4A on linkage group 4A.2 was the most consistent across all environments and explained 40-50% of phenotypic variation. The QTL on 1D is a novel QTL and explained 1.99-2.33% of phenotypic variation. The QTLs on 6B.1 and 6D each explained 3.09-4.33% and 1.62-2.45% of phenotypic variation, respectively. A combination of four stable QTLs on linkage groups 1D, 4A.2, 6B.1 and 6D greatly increased PHS resistance. Allelic effects for the QTLs QPhs.umb-4A, QPhs.umb-6B and QPhs.umb-6D were contributed by RL4137, whereas 'Roblin' contributed the resistant allele for QPhs.umb-1D. QPhs.umb-4A was required for strong dormancy in the 'Roblin'/RL4137 DH population, and the presence of QTLs QPhs.umb-1D, QPhs.umb-6B and QPhs.umb-6D incrementally increased dormancy; DH lines carrying all four QTLs are considerably more dormant than those carrying only QPhs.umb-4A or none of the four QTLs. Thus, the QTLs identified in this study have the potential to improve PHS resistance in spring wheat.
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Affiliation(s)
- M M Uzzal A Liton
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada
| | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Colin W Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Santosh Kumar
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, R7A 5Y3, Canada
| | - Mark C Jordan
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Belay T Ayele
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada.
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Gupta PK, Balyan HS, Sharma S, Kumar R. Genetics of yield, abiotic stress tolerance and biofortification in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1569-1602. [PMID: 32253477 DOI: 10.1007/s00122-020-03583-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/13/2020] [Indexed: 05/18/2023]
Abstract
A review of the available literature on genetics of yield and its component traits, tolerance to abiotic stresses and biofortification should prove useful for future research in wheat in the genomics era. The work reviewed in this article mainly covers the available information on genetics of some important quantitative traits including yield and its components, tolerance to abiotic stresses (heat, drought, salinity and pre-harvest sprouting = PHS) and biofortification (Fe/Zn and phytate contents with HarvestPlus Program) in wheat. Major emphasis is laid on the recent literature on QTL interval mapping and genome-wide association studies, giving lists of known QTL and marker-trait associations. Candidate genes for different traits and the cloned and characterized genes for yield traits along with the molecular mechanism are also described. For each trait, an account of the present status of marker-assisted selection has also been included. The details of available results have largely been presented in the form of tables; some of these tables are included as supplementary files.
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Affiliation(s)
- Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India.
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Rahul Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
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Kumar R, Janila P, Vishwakarma MK, Khan AW, Manohar SS, Gangurde SS, Variath MT, Shasidhar Y, Pandey MK, Varshney RK. Whole-genome resequencing-based QTL-seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:992-1003. [PMID: 31553830 PMCID: PMC7061874 DOI: 10.1111/pbi.13266] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/28/2019] [Accepted: 09/22/2019] [Indexed: 05/11/2023]
Abstract
The subspecies fastigiata of cultivated groundnut lost fresh seed dormancy (FSD) during domestication and human-made selection. Groundnut varieties lacking FSD experience precocious seed germination during harvest imposing severe losses. Development of easy-to-use genetic markers enables early-generation selection in different molecular breeding approaches. In this context, one recombinant inbred lines (RIL) population (ICGV 00350 × ICGV 97045) segregating for FSD was used for deploying QTL-seq approach for identification of key genomic regions and candidate genes. Whole-genome sequencing (WGS) data (87.93 Gbp) were generated and analysed for the dormant parent (ICGV 97045) and two DNA pools (dormant and nondormant). After analysis of resequenced data from the pooled samples with dormant parent (reference genome), we calculated delta-SNP index and identified a total of 10,759 genomewide high-confidence SNPs. Two candidate genomic regions spanning 2.4 Mb and 0.74 Mb on the B05 and A09 pseudomolecules, respectively, were identified controlling FSD. Two candidate genes-RING-H2 finger protein and zeaxanthin epoxidase-were identified in these two regions, which significantly express during seed development and control abscisic acid (ABA) accumulation. QTL-seq study presented here laid out development of a marker, GMFSD1, which was validated on a diverse panel and could be used in molecular breeding to improve dormancy in groundnut.
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Affiliation(s)
- Rakesh Kumar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Surendra S. Manohar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Sunil S. Gangurde
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Murali T. Variath
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Manish K. Pandey
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
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12
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Martinez SA, Shorinola O, Conselman S, See D, Skinner DZ, Uauy C, Steber CM. Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:719-736. [PMID: 31993676 PMCID: PMC7021667 DOI: 10.1007/s00122-019-03503-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/06/2019] [Indexed: 05/09/2023]
Abstract
Using bulked segregant analysis of exome sequence, we fine-mapped the ABA-hypersensitive mutant ERA8 in a wheat backcross population to the TaMKK3-A locus of chromosome 4A. Preharvest sprouting (PHS) is the germination of mature grain on the mother plant when it rains before harvest. The ENHANCED RESPONSE TO ABA8 (ERA8) mutant increases seed dormancy and, consequently, PHS tolerance in soft white wheat 'Zak.' ERA8 was mapped to chromosome 4A in a Zak/'ZakERA8' backcross population using bulked segregant analysis of exome sequenced DNA (BSA-exome-seq). ERA8 was fine-mapped relative to mutagen-induced SNPs to a 4.6 Mb region containing 70 genes. In the backcross population, the ERA8 ABA-hypersensitive phenotype was strongly linked to a missense mutation in TaMKK3-A-G1093A (LOD 16.5), a gene associated with natural PHS tolerance in barley and wheat. The map position of ERA8 was confirmed in an 'Otis'/ZakERA8 but not in a 'Louise'/ZakERA8 mapping population. This is likely because Otis carries the same natural PHS susceptible MKK3-A-A660S allele as Zak, whereas Louise carries the PHS-tolerant MKK3-A-C660R allele. Thus, the variation for grain dormancy and PHS tolerance in the Louise/ZakERA8 population likely resulted from segregation of other loci rather than segregation for PHS tolerance at the MKK3 locus. This inadvertent complementation test suggests that the MKK3-A-G1093A mutation causes the ERA8 phenotype. Moreover, MKK3 was a known ABA signaling gene in the 70-gene 4.6 Mb ERA8 interval. None of these 70 genes showed the differential regulation in wild-type Zak versus ERA8 expected of a promoter mutation. Thus, the working model is that the ERA8 phenotype results from the MKK3-A-G1093A mutation.
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Affiliation(s)
- Shantel A Martinez
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | | | - Samantha Conselman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Deven See
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA
| | - Daniel Z Skinner
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Camille M Steber
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA.
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13
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Zhu Y, Wang S, Wei W, Xie H, Liu K, Zhang C, Wu Z, Jiang H, Cao J, Zhao L, Lu J, Zhang H, Chang C, Xia X, Xiao S, Ma C. Genome-wide association study of pre-harvest sprouting tolerance using a 90K SNP array in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2947-2963. [PMID: 31324930 DOI: 10.1007/s00122-019-03398-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 06/29/2019] [Accepted: 07/11/2019] [Indexed: 05/06/2023]
Abstract
Three major loci for pre-harvest sprouting tolerance (PHST) were mapped on chromosomes 1AL, 3BS, and 6BL, and two CAPS and one dCAPS markers were validated. Sixteen lines with favorable alleles and increased PHST were identified. Pre-harvest sprouting (PHS) significantly affects wheat grain yield and quality. In the present study, the PHS tolerance (PHST) of 192 wheat varieties (lines) was evaluated by assessment of field sprouting, seed germination index, and period of dormancy in different environments. A high-density Illumina iSelect 90K SNP array was used to genotype the panel. A genome-wide association study (GWAS) based on single- and multi-locus mixed linear models was used to detect loci for PHST. The single-locus model identified 23 loci for PHST (P < 0.0001) and explained 6.0-18.9% of the phenotypic variance. Twenty loci were consistent with known quantitative trait loci (QTLs). Three single-nucleotide polymorphism markers closely linked with three major loci (Qphs.ahau-1A, Qphs.ahau-3B, and Qphs.ahau-6B) on chromosomes 1AL, 3BS, and 6BL, respectively, were converted to two cleaved amplified polymorphic sequences (CAPS) and one derived-CAPS markers, and validated in 374 wheat varieties (lines). The CAPS marker EX06323 for Qphs.ahau-6B co-segregated with a novel major QTL underlying PHST in a recombinant inbred line population raised from the cross Jing 411 × Wanxianbaimaizi. Linear regression showed a clear dependence of PHST on the number of favorable alleles. Sixteen varieties showing an elevated degree of PHST were identified and harbored more than 16 favorable alleles. The multi-locus model detected 39 marker-trait associations for PHST (P < 0.0001), of which five may be novel. Six loci common to the two models were identified. The combination of the two GWAS methods contributes to efficient dissection of the complex genetic mechanism of PHST.
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Affiliation(s)
- Yulei Zhu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Shengxing Wang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Wenxin Wei
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Hongyong Xie
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Kai Liu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Can Zhang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Zengyun Wu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Hao Jiang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Jiajia Cao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Liangxia Zhao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Haiping Zhang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China.
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China.
| | - Xianchun Xia
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Shihe Xiao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
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14
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Cheng X, Wang S, Xu D, Liu X, Li X, Xiao W, Cao J, Jiang H, Min X, Wang J, Zhang H, Chang C, Lu J, Ma C. Identification and Analysis of the GASR Gene Family in Common Wheat ( Triticum aestivum L.) and Characterization of TaGASR34, a Gene Associated With Seed Dormancy and Germination. Front Genet 2019; 10:980. [PMID: 31681420 PMCID: PMC6813915 DOI: 10.3389/fgene.2019.00980] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/13/2019] [Indexed: 11/13/2022] Open
Abstract
Seed dormancy and germination are important agronomic traits in wheat (Triticum aestivum L.) because they determine pre-harvest sprouting (PHS) resistance and thus affect grain production. These processes are regulated by Gibberellic Acid-Stimulated Regulator (GASR) genes. In this study, we identified 37 GASR genes in common wheat, which were designated TaGASR1-37. Moreover, we identified 40 pairs of paralogous genes, of which only one had a Ka/Ks value greater than 1, indicating that most TaGASR genes have undergone negative selection. Chromosomal location and duplication analysis revealed 25 pairs of segmentally duplicated genes and seven pairs of tandemly duplicated genes, suggesting that large-scale duplication events may have contributed to the expansion of TaGASR gene family. Microarray analysis of the expression of 18 TaGASR genes indicated that these genes play diverse roles in different biological processes. Using wheat varieties with contrasting seed dormancy phenotypes, we investigated the expression patterns of TaGASR genes and the corresponding seed germination index phenotypes in response to water imbibition, exogenous ABA and GA treatment, and low- and high-temperature treatment. Based on these data, we identified the TaGASR34 gene as potentially associated with seed dormancy and germination. Further, we used a SNP mutation of the TaGASR34 promoter (-16) to develop the CAPS marker GS34-7B, which was then used to validate the association of TaGASR34 with seed dormancy and germination by evaluating two natural populations across environments. Notably, the frequency of the high-dormancy GS34-7Bb allele was significantly lower than that of the low-dormancy GS34-7Ba allele, implying that the favorable GS34-7Bb allele has not previously been used in wheat breeding. These results provide valuable information for further functional analysis of TaGASR genes and present a useful gene and marker combination for future improvement of PHS resistance in wheat.
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Affiliation(s)
- Xinran Cheng
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Shengxing Wang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Dongmei Xu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Xue Liu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Xinyu Li
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Weiwei Xiao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Jiajia Cao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Hao Jiang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Xiaoyu Min
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Jianfeng Wang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Haiping Zhang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
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15
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Genome-Wide Association Study for Multiple Biotic Stress Resistance in Synthetic Hexaploid Wheat. Int J Mol Sci 2019; 20:ijms20153667. [PMID: 31357467 PMCID: PMC6696463 DOI: 10.3390/ijms20153667] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/22/2022] Open
Abstract
Genetic resistance against biotic stress is a major goal in many wheat breeding programs. However, modern wheat cultivars have a limited genetic variation for disease and pest resistance and there is always a possibility of the evolution of new diseases and pests to overcome previously identified resistance genes. A total of 125 synthetic hexaploid wheats (SHWs; 2n = 6x = 42, AABBDD, Triticum aestivum L.) were characterized for resistance to fungal pathogens that cause wheat rusts (leaf; Puccinia triticina, stem; P. graminis f.sp. tritici, and stripe; P. striiformis f.sp. tritici) and crown rot (Fusarium spp.); cereal cyst nematode (Heterodera spp.); and Hessian fly (Mayetiola destructor). A wide range of genetic variation was observed among SHWs for multiple (two to five) biotic stresses and 17 SHWs that were resistant to more than two stresses. The genomic regions and potential candidate genes conferring resistance to these biotic stresses were identified from a genome-wide association study (GWAS). This GWAS study identified 124 significant marker-trait associations (MTAs) for multiple biotic stresses and 33 of these were found within genes. Furthermore, 16 of the 33 MTAs present within genes had annotations suggesting their potential role in disease resistance. These results will be valuable for pyramiding novel genes/genomic regions conferring resistance to multiple biotic stresses from SHWs into elite bread wheat cultivars and providing further insights on a wide range of stress resistance in wheat.
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16
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Zuo J, Lin CT, Cao H, Chen F, Liu Y, Liu J. Genome-wide association study and quantitative trait loci mapping of seed dormancy in common wheat (Triticum aestivum L.). PLANTA 2019; 250:187-198. [PMID: 30972483 DOI: 10.1007/s00425-019-03164-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 04/06/2019] [Indexed: 05/06/2023]
Abstract
Totally, 23 and 26 loci for the first count germination ratio and the final germination ratio were detected by quantitative trait loci (QTL) mapping and association mapping, respectively, which could be used to facilitate wheat pre-harvest sprouting breeding. Weak dormancy can cause pre-harvest sprouting in seeds of common wheat which significantly reduces grain yield. In this study, both quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) were used to identify loci controlling seed dormancy. The analyses were based on a recombinant inbred line population derived from Zhou 8425B/Chinese Spring cross and 166 common wheat accessions. Inclusive composite interval mapping detected 8 QTL, while 45 loci were identified in the 166 wheat accessions by GWAS. Among these, four loci (Qbifcgr.cas-3AS/Qfcgr.cas-3AS, Qbifcgr.cas-6AL.1/Qfcgr.cas-6AL.1, Qbifcgr.cas-7BL.2/Qfcgr.cas-7BL.2, and Qbigr.cas-3DL/Qgr.cas-3DL) were detected in both QTL mapping and GWAS. In addition, 41 loci co-located with QTL reported previously, whereas 8 loci (Qfcgr.cas-5AL, Qfcgr.cas-6DS, Qfcgr.cas-7AS, Qgr.cas-3DS.1, Qgr.cas-3DS.2, Qbigr.cas-3DL/Qgr.cas-3DL, Qgr.cas-4B, and Qgr.cas-5A) were likely to be new. Linear regression showed the first count germination ratio or the final germination ratio reduced while multiple favorable alleles increased. It is suggested that QTL pyramiding was effective to reduce pre-harvest sprouting risk. This study could enrich the research on pre-harvest sprouting and provide valuable information of marker exploration for wheat breeding programs.
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Affiliation(s)
- Jinghong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Science, Beijing, China
| | - Chih-Ta Lin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- College of Life Science, University of Chinese Academy of Science, Beijing, China.
| | - Jindong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
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17
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Unraveling Molecular and Genetic Studies of Wheat (Triticum aestivum L.) Resistance against Factors Causing Pre-Harvest Sprouting. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9030117] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Pre-harvest sprouting (PHS) is one of the most important factors having adverse effects on yield and grain quality all over the world, particularly in wet harvest conditions. PHS is controlled by both genetic and environmental factors and the interaction of these factors. Breeding varieties with high PHS resistance have important implications for reducing yield loss and improving grain quality. The rapid advancements in the wheat genomic database along with transcriptomic and proteomic technologies have broadened our knowledge for understanding the regulatory mechanism of PHS resistance at transcriptomic and post-transcriptomic levels. In this review, we have described in detail the recent advancements on factors influencing PHS resistance, including grain color, seed dormancy, α-amylase activity, plant hormones (especially abscisic acid and gibberellin), and QTL/genes, which are useful for mining new PHS-resistant genes and developing new molecular markers for multi-gene pyramiding breeding of wheat PHS resistance, and understanding the complicated regulatory mechanism of PHS resistance.
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18
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Kumar A, Pathak RK, Gayen A, Gupta S, Singh M, Lata C, Sharma H, Roy JK, Gupta SM. Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security. 3 Biotech 2018; 8:460. [PMID: 30370201 PMCID: PMC6200710 DOI: 10.1007/s13205-018-1483-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/16/2018] [Indexed: 11/28/2022] Open
Abstract
Seeds serve as biochemical factories of nutrition, processing, bio-energy and storage related important bio-molecules and act as a delivery system to transmit the genetic information to the next generation. The research pertaining towards delineating the complex system of regulation of genes and pathways related to seed biology and nutrient partitioning is still under infancy. To understand these, it is important to know the genes and pathway(s) involved in the homeostasis of bio-molecules. In recent past with the advent and advancement of modern tools of genomics and genetic engineering, multi-layered 'omics' approaches and high-throughput platforms are being used to discern the genes and proteins involved in various metabolic, and signaling pathways and their regulations for understanding the molecular genetics of biosynthesis and homeostasis of bio-molecules. This can be possible by exploring systems biology approaches via the integration of omics data for understanding the intricacy of seed development and nutrient partitioning. These information can be exploited for the improvement of biologically important chemicals for large-scale production of nutrients and nutraceuticals through pathway engineering and biotechnology. This review article thus describes different omics tools and other branches that are merged to build the most attractive area of research towards establishing the seeds as biochemical factories for human health and nutrition.
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Affiliation(s)
- Anil Kumar
- Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Aranyadip Gayen
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Supriya Gupta
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Manoj Singh
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Charu Lata
- Council of Scientific and Industrial Research-National Botanical Research Institute, Lucknow, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Joy Kumar Roy
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Sanjay Mohan Gupta
- Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio-Energy Research (DIBER), DRDO, Haldwani, 263139 India
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19
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Du L, Xu F, Fang J, Gao S, Tang J, Fang S, Wang H, Tong H, Zhang F, Chu J, Wang G, Chu C. Endosperm sugar accumulation caused by mutation of PHS8/ISA1 leads to pre-harvest sprouting in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:545-556. [PMID: 29775500 DOI: 10.1111/tpj.13970] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 05/18/2023]
Abstract
Pre-harvest sprouting (PHS) is an unfavorable trait in cereal crops that could seriously decrease grain yield and quality. Although some PHS-associated quantitative trait loci or genes in cereals have been reported, the molecular mechanism underlying PHS remains largely elusive. Here, we characterized a rice mutant, phs8, which exhibits PHS phenotype accompanied by sugary endosperm. Map-based cloning revealed that PHS8 encodes a starch debranching enzyme named isoamylase1. Mutation in PHS8 resulted in the phytoglycogen breakdown and sugar accumulation in the endosperm. Intriguingly, with increase of sugar contents, decreased expression of OsABI3 and OsABI5 as well as reduced sensitivity to abscisic acid (ABA) were found in the phs8 mutant. Using rice suspension cell system, we confirmed that exogenous sugar is sufficient to suppress the expression of both OsABI3 and OsABI5. Furthermore, overexpression of OsABI3 or OsABI5 could partially rescue the PHS phenotype of phs8. Therefore, our study presents important evidence supporting that endosperm sugar not only acts as an essential energy source for seed germination but also determines seed dormancy and germination by affecting ABA signaling.
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Affiliation(s)
- Lin Du
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fan Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Fang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shaopei Gao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiuyou Tang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuang Fang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongru Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongning Tong
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fengxia Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfang Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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Martinez SA, Godoy J, Huang M, Zhang Z, Carter AH, Garland Campbell KA, Steber CM. Genome-Wide Association Mapping for Tolerance to Preharvest Sprouting and Low Falling Numbers in Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:141. [PMID: 29491876 PMCID: PMC5817628 DOI: 10.3389/fpls.2018.00141] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/25/2018] [Indexed: 05/19/2023]
Abstract
Preharvest sprouting (PHS), the germination of grain on the mother plant under cool and wet conditions, is a recurring problem for wheat farmers worldwide. α-amylase enzyme produced during PHS degrades starch resulting in baked good with poor end-use quality. The Hagberg-Perten Falling Number (FN) test is used to measure this problem in the wheat industry, and determines how much a farmer's wheat is discounted for PHS damage. PHS tolerance is associated with higher grain dormancy. Thus, breeding programs use germination-based assays such as the spike-wetting test to measure PHS susceptibility. Association mapping identified loci associated with PHS tolerance in U.S. Pacific Northwest germplasm based both on FN and on spike-wetting test data. The study was performed using a panel of 469 white winter wheat cultivars and elite breeding lines grown in six Washington state environments, and genotyped for 15,229 polymorphic markers using the 90k SNP Illumina iSelect array. Marker-trait associations were identified using the FarmCPU R package. Principal component analysis was directly and a kinship matrix was indirectly used to account for population structure. Nine loci were associated with FN and 34 loci associated with PHS based on sprouting scores. None of the QFN.wsu loci were detected in multiple environments, whereas six of the 34 QPHS.wsu loci were detected in two of the five environments. There was no overlap between the QTN detected based on FN and PHS, and there was little correlation between the two traits. However, both traits appear to be PHS-related since 19 of the 34 QPHS.wsu loci and four of the nine QFN.wsu loci co-localized with previously published dormancy and PHS QTL. Identification of these loci will lead to a better understanding of the genetic architecture of PHS and will help with the future development of genomic selection models.
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Affiliation(s)
- Shantel A. Martinez
- Molecular Plant Sciences, Washington State University, Pullman, WA, United States
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Jayfred Godoy
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Meng Huang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Zhiwu Zhang
- Molecular Plant Sciences, Washington State University, Pullman, WA, United States
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Arron H. Carter
- Molecular Plant Sciences, Washington State University, Pullman, WA, United States
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Kimberly A. Garland Campbell
- Molecular Plant Sciences, Washington State University, Pullman, WA, United States
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
- USDA-ARS Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, WA, United States
| | - Camille M. Steber
- Molecular Plant Sciences, Washington State University, Pullman, WA, United States
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
- USDA-ARS Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, WA, United States
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Dale Z, Jie H, Luyu H, Cancan Z, Yun Z, Yarui S, Suoping L. An Advanced Backcross Population through Synthetic Octaploid Wheat as a "Bridge": Development and QTL Detection for Seed Dormancy. FRONTIERS IN PLANT SCIENCE 2017; 8:2123. [PMID: 29321790 PMCID: PMC5733556 DOI: 10.3389/fpls.2017.02123] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/29/2017] [Indexed: 05/21/2023]
Abstract
The seed dormancy characteristic is regarded as one of the most critical factors for pre-harvest sprouting (PHS) resistance. As a wild wheat relative species, Aegilops tauschii is a potential genetic resource for improving common wheat. In this study, an advanced backcross population (201 strains) containing only Ae. tauschii segments was developed by means of synthetic octaploid wheat (hexaploid wheat Zhoumai 18 × Ae. tauschii T093). Subsequently, seed dormancy rate (Dor) in the advanced backcross population was evaluated on the day 3, 5 and 7, in which 2 major QTLs (QDor-2D and QDor-3D) were observed on chromosomes 2D and 3D with phenotypic variance explained values (PVEs) of 10.25 and 20.40%, respectively. Further investigation revealed significant correlation between QDor-3D and Tamyb10 gene, while no association was found between the former and TaVp1 gene, implying that QDor-3D site could be of closer position to Tamyb10. The obtained quantitative trait locus sites (QTLs) in this work could be applied to develop wheat cultivars with PHS resistance.
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Affiliation(s)
- Zhang Dale
- School of Life Science, Henan University, Kaifeng, China
- Institute of Plant Stress Biology, Henan University, Kaifeng, China
| | - He Jie
- School of Life Science, Henan University, Kaifeng, China
| | - Huang Luyu
- School of Life Science, Henan University, Kaifeng, China
| | - Zhang Cancan
- School of Life Science, Henan University, Kaifeng, China
| | - Zhou Yun
- School of Life Science, Henan University, Kaifeng, China
- Institute of Plant Stress Biology, Henan University, Kaifeng, China
| | - Su Yarui
- School of Life Science, Henan University, Kaifeng, China
| | - Li Suoping
- School of Life Science, Henan University, Kaifeng, China
- Institute of Plant Stress Biology, Henan University, Kaifeng, China
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Kocheshkova AA, Kroupin PY, Bazhenov MS, Karlov GI, Pochtovyy AA, Upelniek VP, Belov VI, Divashuk MG. Pre-harvest sprouting resistance and haplotype variation of ThVp-1 gene in the collection of wheat-wheatgrass hybrids. PLoS One 2017; 12:e0188049. [PMID: 29131854 PMCID: PMC5683615 DOI: 10.1371/journal.pone.0188049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/31/2017] [Indexed: 11/19/2022] Open
Abstract
The germplasm collection of 87 wheat-wheatgrass hybrids developed in Tsitisin Main Botanical Garden (Russia, Moscow) was evaluated for resistance to pre-harvest sprouting (PHS) by spike sprouting (SS) and germination index (GI) assays as well as for spike and grain features. The PHS resistance variation and haplotype polymorphism of the wheatgrass ThVp-1 and wheat TaVp-1B genes orthologues of Vp-1 was revealed in the studied collection. Four haplotypes of ThVp-1 were revealed: ThVp-1a (41% of the entries), ThVp-1b (13%), ThVp-1c (29%), and ThVp-1d (15%). The association between the allelic state of ThVp-1 and PHS resistance in the wheat-wheatgrass hybrids was shown: haplotype ThVp-1d of the wheatgrass Vp-1 gene is significantly associated with reduced PHS in the wheat-wheatgrass hybrids (mean SS 0.33, mean GI 0.64). The resistant entries may be perspective as a source of PHS resistance in the development of commercial cultivars of perennial wheat.
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Affiliation(s)
- A. A. Kocheshkova
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - P. Yu. Kroupin
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - M. S. Bazhenov
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - G. I. Karlov
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - A. A. Pochtovyy
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - V. P. Upelniek
- Department of Distant Hybridization, N. V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, Moscow, Russia
| | - V. I. Belov
- Department of Distant Hybridization, N. V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, Moscow, Russia
| | - M. G. Divashuk
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
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23
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Macovei A, Pagano A, Leonetti P, Carbonera D, Balestrazzi A, Araújo SS. Systems biology and genome-wide approaches to unveil the molecular players involved in the pre-germinative metabolism: implications on seed technology traits. PLANT CELL REPORTS 2017; 36:669-688. [PMID: 27730302 DOI: 10.1007/s00299-016-2060-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/26/2016] [Indexed: 05/21/2023]
Abstract
The pre-germinative metabolism is among the most fascinating aspects of seed biology. The early seed germination phase, or pre-germination, is characterized by rapid water uptake (imbibition), which directs a series of dynamic biochemical events. Among those are enzyme activation, DNA damage and repair, and use of reserve storage compounds, such as lipids, carbohydrates and proteins. Industrial seedling production and intensive agricultural production systems require seed stocks with high rate of synchronized germination and low dormancy. Consequently, seed dormancy, a quantitative trait related to the activation of the pre-germinative metabolism, is probably the most studied seed trait in model species and crops. Single omics, systems biology, QTLs and GWAS mapping approaches have unveiled a list of molecules and regulatory mechanisms acting at transcriptional, post-transcriptional and post-translational levels. Most of the identified candidate genes encode for regulatory proteins targeting ROS, phytohormone and primary metabolisms, corroborating the data obtained from simple molecular biology approaches. Emerging evidences show that epigenetic regulation plays a crucial role in the regulation of these mentioned processes, constituting a still unexploited strategy to modulate seed traits. The present review will provide an up-date of the current knowledge on seed pre-germinative metabolism, gathering the most relevant results from physiological, genetics, and omics studies conducted in model and crop plants. The effects exerted by the biotic and abiotic stresses and priming are also addressed. The possible implications derived from the modulation of pre-germinative metabolism will be discussed from the point of view of seed quality and technology.
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Affiliation(s)
- Anca Macovei
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Andrea Pagano
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Paola Leonetti
- Institute for Sustainable Plant Protection, National Council of Research, via Amendola 122/D, 70126, Bari, Italy
| | - Daniela Carbonera
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Susana S Araújo
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
- Plant Cell Biotechnology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Av. da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal.
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Zhang Y, Xia X, He Z. The seed dormancy allele TaSdr-A1a associated with pre-harvest sprouting tolerance is mainly present in Chinese wheat landraces. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:81-89. [PMID: 27650191 DOI: 10.1007/s00122-016-2793-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/24/2016] [Indexed: 05/06/2023]
Abstract
We cloned TaSdr - A1 gene, and developed a gene-specific marker for TaSdr - A1 . A QTL for germination index at the TaSdr - A1 locus was identified in the Yangxiaomai/Zhongyou 9507 RIL population. Pre-harvest sprouting (PHS) affects yield and end-use quality in bread wheat (Triticum aestivum L.). In the present study we found an association between the TaSdr-A1 gene and PHS tolerance in bread wheat. TaSdr-A1 on chromosome 2A was cloned using a homologous cloning approach. Sequence analysis of TaSdr-A1 revealed an SNP at position 643, with the G allele being present in genotypes with lower germination index (GI) values and A in those with higher GI. These alleles were designated as TaSdr-A1a and TaSdr-A1b, respectively. A cleaved amplified polymorphism sequence (CAPS) marker Sdr2A based on the SNP was developed, and linkage mapping and QTL analysis were conducted to confirm the association between TaSdr-A1 and seed dormancy. Sdr2A was located in a 2.9 cM interval between SSR markers Xgwm95 and Xgwm372. A QTL for GI at the TaSdr-A1 locus explained 6.6, 7.3, and 8.2 % of the phenotypic variances in a Yangxiaomai/Zhongyou 9507 RIL population grown at Beijing, Shijiazhuang, and the averaged data from the two environments, respectively. Two sets of Chinese wheat cultivars used for validating the TaSdr-A1 polymorphism and the corresponding gene-specific marker Sdr2A showed that TaSdr-A1 was significantly associated with GI. Among 29 accessions with TaSdr-A1a, 24 (82.8 %) were landraces, indicating the importance of Chinese wheat landraces as sources of PHS tolerance. This study identified a novel PHS resistance allele TaSdr-A1a mainly presented in Chinese landraces and it is likely to be the causal gene for QPhs.ccsu-2A.3, providing new information for an understanding of seed dormancy.
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Affiliation(s)
- Yingjun Zhang
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, 162 Hengshan Street, Shijiazhuang, 050035, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
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25
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Zhou Y, Tang H, Cheng MP, Dankwa KO, Chen ZX, Li ZY, Gao S, Liu YX, Jiang QT, Lan XJ, Pu ZE, Wei YM, Zheng YL, Hickey LT, Wang JR. Genome-Wide Association Study for Pre-harvest Sprouting Resistance in a Large Germplasm Collection of Chinese Wheat Landraces. FRONTIERS IN PLANT SCIENCE 2017; 8:401. [PMID: 28428791 PMCID: PMC5382224 DOI: 10.3389/fpls.2017.00401] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/09/2017] [Indexed: 05/06/2023]
Abstract
Pre-harvest sprouting (PHS) is mainly caused by the breaking of seed dormancy in high rainfall regions, which leads to huge economic losses in wheat. In this study, we evaluated 717 Chinese wheat landraces for PHS resistance and carried out genome-wide association studies (GWAS) using to 9,740 DArT-seq and 178,803 SNP markers. Landraces were grown across six environments in China and germination testing of harvest-ripe grain was used to calculate the germination rate (GR) for each accession at each site. GR was highly correlated across all environments. A large number of landraces (194) displayed high levels of PHS resistance (i.e., mean GR < 0.20), which included nine white-grained accessions. Overall, white-grained accessions displayed a significantly higher mean GR (42.7-79.6%) compared to red-grained accessions (19.1-56.0%) across the six environments. Landraces from mesic growing zones in southern China showed higher levels of PHS resistance than those sourced from xeric areas in northern and north-western China. Three main quantitative trait loci (QTL) were detected by GWAS: one on 5D that appeared to be novel and two co-located with the grain color transcription factor Tamyb10 on 3A and 3D. An additional 32 grain color related QTL (GCR-QTL) were detected when the set of red-grained landraces were analyzed separately. GCR-QTL occurred at high frequencies in the red-grained accessions and a strong correlation was observed between the number of GCR-QTL and GR (R2 = 0.62). These additional factors could be critical for maintaining high levels of PHS resistance and represent targets for introgression into white-grained wheat cultivars. Further, investigation of the origin of haplotypes associated with the three main QTL revealed that favorable haplotypes for PHS resistance were more common in accessions from higher rainfall zones in China. Thus, a combination of natural and artificial selection likely resulted in landraces incorporating PHS resistance in China.
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Affiliation(s)
- Yong Zhou
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Hao Tang
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Meng-Ping Cheng
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Kwame O. Dankwa
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Zhong-Xu Chen
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Zhan-Yi Li
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Shang Gao
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Ya-Xi Liu
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Xiu-Jin Lan
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Zhi-En Pu
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural UniversityYa’an, China
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, BrisbaneQLD, Australia
| | - Ji-Rui Wang
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
- *Correspondence: Ji-Rui Wang,
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26
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Lin M, Zhang D, Liu S, Zhang G, Yu J, Fritz AK, Bai G. Genome-wide association analysis on pre-harvest sprouting resistance and grain color in U.S. winter wheat. BMC Genomics 2016; 17:794. [PMID: 27729004 PMCID: PMC5059910 DOI: 10.1186/s12864-016-3148-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 10/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pre-harvest sprouting (PHS) in wheat can cause substantial reduction in grain yield and end-use quality. Grain color (GC) together with other components affect PHS resistance. Several quantitative trait loci (QTL) have been reported for PHS resistance, and two of them on chromosome 3AS (TaPHS1) and 4A have been cloned. METHODS To determine genetic architecture of PHS and GC and genetic relationships of the two traits, a genome-wide association study (GWAS) was conducted by evaluating a panel of 185 U.S. elite breeding lines and cultivars for sprouting rates of wheat spikes and GC in both greenhouse and field experiments. The panel was genotyped using the wheat 9K and 90K single nucleotide polymorphism (SNP) arrays. RESULTS Four QTL for GC on four chromosomes and 12 QTL for PHS resistance on 10 chromosomes were identified in at least two experiments. QTL for PHS resistance showed varied effects under different environments, and those on chromosomes 3AS, 3AL, 3B, 4AL and 7A were the more frequently identified QTL. The common QTL for GC and PHS resistance were identified on the long arms of the chromosome 3A and 3D. CONCLUSIONS Wheat grain color is regulated by the three known genes on group 3 chromosomes and additional genes from other chromosomes. These grain color genes showed significant effects on PHS resistance in some environments. However, several other QTL that did not affect grain color also played a significant role on PHS resistance. Therefore, it is possible to breed PHS-resistant white wheat by pyramiding these non-color related QTL.
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Affiliation(s)
- Meng Lin
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Dadong Zhang
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Shubing Liu
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Guorong Zhang
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Jianming Yu
- Agronomy Department, Iowa State University Ames, Iowa, 50011, USA
| | - Allan K Fritz
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Guihua Bai
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA. .,Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506, USA.
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27
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Burke M, Small DM, Antolasic F, Hughes JG, Spencer MJS, Blanch EW, Jones OAH. Infrared Spectroscopy-Based Metabolomic Analysis for the Detection of Preharvest Sprouting in Grain. Cereal Chem 2016. [DOI: 10.1094/cchem-01-16-0005-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Matthew Burke
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, GPO Box 2476, Melbourne, VIC 3001, Australia
| | - Darryl M. Small
- School of Science, RMIT University, GPO Box 2476, Melbourne, VIC 3001, Australia
| | - Frank Antolasic
- School of Science, RMIT University, GPO Box 2476, Melbourne, VIC 3001, Australia
| | - Jeff G. Hughes
- School of Science, RMIT University, GPO Box 2476, Melbourne, VIC 3001, Australia
| | | | - Ewan W. Blanch
- School of Science, RMIT University, GPO Box 2476, Melbourne, VIC 3001, Australia
| | - Oliver A. H. Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, GPO Box 2476, Melbourne, VIC 3001, Australia
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28
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Shorinola O, Bird N, Simmonds J, Berry S, Henriksson T, Jack P, Werner P, Gerjets T, Scholefield D, Balcárková B, Valárik M, Holdsworth MJ, Flintham J, Uauy C. The wheat Phs-A1 pre-harvest sprouting resistance locus delays the rate of seed dormancy loss and maps 0.3 cM distal to the PM19 genes in UK germplasm. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4169-78. [PMID: 27217549 PMCID: PMC5301926 DOI: 10.1093/jxb/erw194] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The precocious germination of cereal grains before harvest, also known as pre-harvest sprouting, is an important source of yield and quality loss in cereal production. Pre-harvest sprouting is a complex grain defect and is becoming an increasing challenge due to changing climate patterns. Resistance to sprouting is multi-genic, although a significant proportion of the sprouting variation in modern wheat cultivars is controlled by a few major quantitative trait loci, including Phs-A1 in chromosome arm 4AL. Despite its importance, little is known about the physiological basis and the gene(s) underlying this important locus. In this study, we characterized Phs-A1 and show that it confers resistance to sprouting damage by affecting the rate of dormancy loss during dry seed after-ripening. We show Phs-A1 to be effective even when seeds develop at low temperature (13 °C). Comparative analysis of syntenic Phs-A1 intervals in wheat and Brachypodium uncovered ten orthologous genes, including the Plasma Membrane 19 genes (PM19-A1 and PM19-A2) previously proposed as the main candidates for this locus. However, high-resolution fine-mapping in two bi-parental UK mapping populations delimited Phs-A1 to an interval 0.3 cM distal to the PM19 genes. This study suggests the possibility that more than one causal gene underlies this major pre-harvest sprouting locus. The information and resources reported in this study will help test this hypothesis across a wider set of germplasm and will be of importance for breeding more sprouting resilient wheat varieties.
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Affiliation(s)
| | - Nicholas Bird
- John Innes Centre, Norwich Research Park, NR4 7UH, UK KWS UK Ltd, Hertfordshire, SG8 7RE, UK
| | | | - Simon Berry
- Limagrain UK Ltd, Woolpit Business Park, IP30 9UP, UK
| | | | | | | | - Tanja Gerjets
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, LE12 5RD, UK
| | - Duncan Scholefield
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, LE12 5RD, UK
| | - Barbara Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - M J Holdsworth
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, LE12 5RD, UK
| | - John Flintham
- John Innes Centre, Norwich Research Park, NR4 7UH, UK
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Torada A, Koike M, Ogawa T, Takenouchi Y, Tadamura K, Wu J, Matsumoto T, Kawaura K, Ogihara Y. A Causal Gene for Seed Dormancy on Wheat Chromosome 4A Encodes a MAP Kinase Kinase. Curr Biol 2016; 26:782-7. [PMID: 26948878 DOI: 10.1016/j.cub.2016.01.063] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/13/2015] [Accepted: 01/22/2016] [Indexed: 12/27/2022]
Abstract
Seed germination under the appropriate environmental conditions is important both for plant species survival and for successful agriculture. Seed dormancy, which controls germination time, is one of the adaptation mechanisms and domestication traits [1]. Seed dormancy is generally defined as the absence of germination of a viable seed under conditions that are favorable for germination [2]. The seed dormancy of cultivated plants has generally been reduced during domestication [3]. Bread wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Weak dormancy may be an advantage for the productivity due to uniform emergence and a disadvantage for the risks of pre-harvest sprouting (PHS), which decreases grain quality and yield [4]. A number of quantitative trait loci (QTLs) controlling natural variation of seed dormancy have been identified on various chromosomes [5]. A major QTL for seed dormancy has been consistently detected on chromosome 4A [6-13]. The QTL was designated as a major gene, Phs1, which could be precisely mapped within a 2.6 cM region [14]. Here, we identified a mitogen-activated protein kinase kinase 3 (MKK3) gene (designated TaMKK3-A) by a map-based approach as a candidate gene for the seed dormancy locus Phs1 on chromosome 4A in bread wheat. Complementation analysis showed that transformation of a dormant wheat cultivar with the TaMKK3-A allele from a nondormant cultivar clearly reduced seed dormancy. Cultivars differing in dormancy had a single nonsynonymous amino acid substitution in the kinase domain of the predicted MKK3 protein sequence, which may be associated with the length of seed dormancy.
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Affiliation(s)
- Atsushi Torada
- HOKUREN Agricultural Research Institute, Naganuma, Hokkaido 069-1317, Japan.
| | - Michiya Koike
- HOKUREN Agricultural Research Institute, Naganuma, Hokkaido 069-1317, Japan
| | - Taiichi Ogawa
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Yu Takenouchi
- HOKUREN Agricultural Research Institute, Naganuma, Hokkaido 069-1317, Japan
| | - Kazuki Tadamura
- HOKUREN Agricultural Research Institute, Naganuma, Hokkaido 069-1317, Japan
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
| | - Yasunari Ogihara
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
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Cao L, Hayashi K, Tokui M, Mori M, Miura H, Onishi K. Detection of QTLs for traits associated with pre-harvest sprouting resistance in bread wheat (Triticum aestivum L.). BREEDING SCIENCE 2016; 66:260-70. [PMID: 27162497 PMCID: PMC4785003 DOI: 10.1270/jsbbs.66.260] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/26/2015] [Indexed: 05/20/2023]
Abstract
Pre-harvest sprouting (PHS) is one of the serious problems for wheat production, especially in rainy regions. Although seed dormancy is the most critical trait for PHS resistance, the control of heading time should also be considered to prevent seed maturation during unfavorable conditions. In addition, awning is known to enhance water absorption by the spike, causing PHS. In this study, we conducted QTL analysis for three PHS resistant related traits, seed dormancy, heading time and awn length, by using recombinant inbred lines from 'Zenkouji-komugi' (high PHS resistance) × 'Chinese Spring' (weak PHS resistance). QTLs for seed dormancy were detected on chromosomes 1B (QDor-1B) and 4A (QDor-4A), in addition to a QTL on chromosome 3A, which was recently cloned as TaMFT-3A. In addition, the accumulation of the QTLs and their epistatic interactions contributed significantly to a higher level of dormancy. QDor-4A is co-located with the Hooded locus for awn development. Furthermore, an effective QTL, which confers early heading by the Zenkouji-komugi allele, was detected on the short arm of chromosome 7B, where the Vrn-B3 locus is located. Understanding the genetic architecture of traits associated with PHS resistance will facilitate the marker assisted selection to breed new varieties with higher PHS resistance.
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31
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Liu S, Sehgal SK, Lin M, Li J, Trick HN, Gill BS, Bai G. Independent mis-splicing mutations in TaPHS1 causing loss of preharvest sprouting (PHS) resistance during wheat domestication. THE NEW PHYTOLOGIST 2015; 208:928-35. [PMID: 26255630 DOI: 10.1111/nph.13489] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/30/2015] [Indexed: 05/19/2023]
Abstract
Preharvest sprouting (PHS) is one of the major constraints of wheat production in areas where prolonged rainfall occurs during harvest. TaPHS1 is a gene that regulates PHS resistance on chromosome 3A of wheat, and two causal mutations in the positions +646 and +666 of the TaPHS1 coding region result in wheat PHS susceptibility. Three competitive allele-specific PCR (KASP) markers were developed based on the two mutations in the coding region and one in the promoter region and validated in 82 wheat cultivars with known genotypes. These markers can be used to transfer TaPHS1 in breeding through marker-assisted selection. Screening of 327 accessions of wheat A genome progenitors using the three KASP markers identified different haplotypes in both diploid and tetraploid wheats. Only one Triticum monococcum accession, however, carries both causal mutations in the TaPHS1 coding region and shows PHS susceptibility. Five of 249 common wheat landraces collected from the Fertile Crescent and surrounding areas carried the mutation (C) in the promoter (-222), and one landrace carries both the causal mutations in the TaPHS1 coding region, indicating that the mis-splicing (+646) mutation occurred during common wheat domestication. PHS assay of wheat progenitor accessions demonstrated that the wild-types were highly PHS-resistant, whereas the domesticated type showed increased PHS susceptibility. The mis-splicing TaPHS1 mutation for PHS susceptibility was involved in wheat domestication and might arise independently between T. monococcum and Triticum aestivum.
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Affiliation(s)
- Shubing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Sunish K Sehgal
- Department of Plant Science, South Dakota State University, Brookings, SD, 57006, USA
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Meng Lin
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Jiarui Li
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
- Hard Winter Wheat Genetic Research Unit, USDA-ARS, Manhattan, KS, 66506, USA
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Lin M, Cai S, Wang S, Liu S, Zhang G, Bai G. Genotyping-by-sequencing (GBS) identified SNP tightly linked to QTL for pre-harvest sprouting resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1385-95. [PMID: 25851002 DOI: 10.1007/s00122-015-2513-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 03/27/2015] [Indexed: 05/03/2023]
Abstract
Using a GBS-SNP map, a QTL for pre-harvest sprouting resistance on 4AL of Totoumai A was delimited to 2.9-cM interval, and SNP closely linked to several other QTL were identified. Pre-harvest sprouting (PHS) of wheat is a major constraint to wheat production in many wheat-growing areas worldwide, because it reduces both wheat grain yield and the end-use quality. To identify markers tightly linked to the quantitative trait loci (QTL) for PHS resistance and seed dormancy (SD), we evaluated 155 recombinant inbred lines (RIL) derived from a cross between a PHS-resistant parent 'Tutoumai A' and a PHS-susceptible parent 'Siyang 936' for single-nucleotide polymorphisms (SNP) using genotyping-by-sequencing (GBS), and for PHS resistance and SD using both field and greenhouse grown plants. Two SNP, GBS109947 and GBS212432, were mapped to a major QTL region for PHS resistance and SD on chromosome 4AL, and delimited the QTL to a 2.9-cM interval. Two and nine additional SNP were mapped to minor QTL regions for SD on chromosome 5B and 5A, respectively. Critical SNP in these QTL regions were converted into KBioscience Competitive Allele-Specific PCR (KASP) assays that can be easily used for marker-assisted selection to improve PHS resistance.
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Affiliation(s)
- Meng Lin
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA
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Albrecht T, Oberforster M, Kempf H, Ramgraber L, Schacht J, Kazman E, Zechner E, Neumayer A, Hartl L, Mohler V. Genome-wide association mapping of preharvest sprouting resistance in a diversity panel of European winter wheats. J Appl Genet 2015; 56:277-85. [PMID: 25924791 DOI: 10.1007/s13353-015-0286-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/08/2015] [Accepted: 04/13/2015] [Indexed: 12/01/2022]
Abstract
Global wheat production will benefit from cultivars showing genetic resistance to preharvest sprouting (PHS). Working on PHS resistance is still challenging due to the lack of simple protocols for the provocation of symptoms for appropriate trait differentiation under highly variable environmental conditions. Therefore, the availability of molecular markers for enhancing PHS resistance in breeding lines is of utmost importance. Genome-wide association mapping was performed to unravel the genetics of PHS resistance in a diversity panel of 124 winter wheat genotypes using both random and targeted marker locus approaches. Data for grain germination tests, spike wetting treatments, and field sprouting damage measurements of grains were collected in 11, 12, and four environments, respectively. Twenty-two quantitative trait loci (QTL) linked with 40 markers were detected for the three traits commonly used for assessing the PHS resistance of cultivars. All but five QTL on chromosomes 1B, 1D (two QTL), 3D, and 5D showed locations similar to previous studies, including prominent QTL on chromosomes 2BS, 3AS, and 4AL. The highest retrieval rate across environments was found for QTL on chromosomes 1D, 2BS, 3D, 4AL, and 7B. The study identified genomic signatures useful for marker-assisted improvement of PHS resistance not only in European breeding programs, but of global significance.
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Affiliation(s)
- Theresa Albrecht
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture (LfL), Am Gereuth 8, 85354, Freising, Germany
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Cabral AL, Jordan MC, McCartney CA, You FM, Humphreys DG, MacLachlan R, Pozniak CJ. Identification of candidate genes, regions and markers for pre-harvest sprouting resistance in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2014; 14:340. [PMID: 25432597 PMCID: PMC4253633 DOI: 10.1186/s12870-014-0340-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/18/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND Pre-harvest sprouting (PHS) of wheat grain leads to a reduction in grain yield and quality. The availability of markers for marker-assisted selection (MAS) of PHS resistance will serve to enhance breeding selection and advancement of lines for cultivar development. The aim of this study was to identify candidate regions and develop molecular markers for PHS resistance in wheat. This was achieved via high density mapping of single nucleotide polymorphism (SNP) markers from an Illumina 90 K Infinium Custom Beadchip in a doubled haploid (DH) population derived from a RL4452/'AC Domain' cross and subsequent detection of quantitative trait loci (QTL) for PHS related traits (falling number [FN], germination index [GI] and sprouting index [SI]). SNP marker sequences flanking QTL were used to locate colinear regions in Brachypodium and rice, and identify genic markers associated with PHS resistance that can be utilized for MAS in wheat. RESULTS A linkage map spanning 2569.4 cM was constructed with a total of 12,201 SNP, simple sequence repeat (SSR), diversity arrays technology (DArT) and expressed sequence tag (EST) markers. QTL analyses using Multiple Interval Mapping (MIM) identified four QTL for PHS resistance traits on chromosomes 3B, 4A, 7B and 7D. Sequences of SNPs flanking these QTL were subject to a BLASTN search on the International Wheat Genome Sequencing Consortium (IWGSC) database (http://wheat-urgi.versailles.inra.fr/Seq-Repository). Best survey sequence hits were subject to a BLASTN search on Gramene (www.gramene.org) against both Brachypodium and rice databases, and candidate genes and regions for PHS resistance were identified. A total of 18 SNP flanking sequences on chromosomes 3B, 4A, 7B and 7D were converted to KASP markers and validated with matching genotype calls of Infinium SNP data. CONCLUSIONS Our study identified candidate genes involved in abscissic acid (ABA) and gibberellin (GA) metabolism, and flowering time in four genomic regions of Brachypodium and rice respectively, in addition to 18 KASP markers for PHS resistance in wheat. These markers can be deployed in future genetic studies of PHS resistance and might also be useful in the evaluation of PHS in germplasm and breeding material.
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Affiliation(s)
- Adrian L Cabral
- />Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada
- />National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Mark C Jordan
- />Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada
| | - Curt A McCartney
- />Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada
| | - Frank M You
- />Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada
| | - D Gavin Humphreys
- />Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada
| | - Ron MacLachlan
- />Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Curtis J Pozniak
- />Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
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35
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Somyong S, Ishikawa G, Munkvold JD, Tanaka J, Benscher D, Cho YG, Sorrells ME. Fine mapping of a preharvest sprouting QTL interval on chromosome 2B in white wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1843-55. [PMID: 24985065 DOI: 10.1007/s00122-014-2345-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 06/07/2014] [Indexed: 05/03/2023]
Abstract
Fine mapping by recombinant backcross populations revealed that a preharvest sprouting QTL on 2B contained two QTLs linked in coupling with different effects on the phenotype. Wheat preharvest sprouting (PHS) occurs when grain germinates on the plant before harvest, resulting in reduced grain quality. Previous mapping of quantitative trait locus (QTL) revealed a major PHS QTL, QPhs.cnl-2B.1, located on chromosome 2B significant in 16 environments that explained from 5 to 31 % of the phenotypic variation. The objective of this project was to fine map the QPhs.cnl-2B.1 interval. Fine mapping was carried out in recombinant backcross populations (BC1F4 and BC1F5) that were developed by backcrossing selected doubled haploids to a recurrent parent and self-pollinating the BC1F4 and BC1F5 generations. In each generation, three markers in the QPhs.cnl-2B.1 interval were used to screen for recombinants. Fine mapping revealed that the QPhs.cnl-2B.1 interval contained two PHS QTLs linked in coupling. The distal PHS QTL, located between Wmc453c and Barc55, contributed 8 % of the phenotypic variation and also co-located with a major seed dormancy QTL determined by germination index. The proximal PHS QTL, between Wmc474 and CNL415-rCDPK, contributed 16 % of the variation. Several candidate genes including Mg-chelatase H subunit family protein, GTP-binding protein and calmodulin/Ca(2+)-dependent protein kinase were linked to the PHS QTL. Although many recombinant lines were identified, the lack of polymorphism for markers in the QTL interval prevented the localization of the recombination breakpoints and identification of the gene underlying the phenotype.
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Affiliation(s)
- Suthasinee Somyong
- Department of Plant Breeding and Genetics, Cornell University, 240 Emerson Hall, Ithaca, NY, 14853, USA
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Singh AK, Knox RE, Clarke JM, Clarke FR, Singh A, DePauw RM, Cuthbert RD. Genetics of pre-harvest sprouting resistance in a cross of Canadian adapted durum wheat genotypes. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 33:919-929. [PMID: 24659906 PMCID: PMC3956934 DOI: 10.1007/s11032-013-0006-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 12/11/2013] [Indexed: 05/06/2023]
Abstract
Severe losses attributable to pre-harvest sprouting (PHS) have been reported in Canada in recent years. The genetics of PHS resistance have been more extensively studied in hexaploid wheat and generally not using combinations of elite agronomic parents. The objective of our research was to understand the genetic nature of PHS resistance in an elite durum cross. A doubled haploid (DH) population and checks were phenotyped in replicated trials for grain yield and PHS traits over 3 years in western Canada. The response of intact spikes to sprouting conditions, sampled over two development time points, was measured in a rain simulation chamber. The DH population was genotyped with simple sequence repeat and Diversity Arrays Technology markers. Genotypes were a significant source of variation for grain yield and PHS resistance traits in each tested environment. Transgressive segregant DH genotypes were identified for grain yield and PHS resistance measurements. Low or no correlation was detected between grain yield and PHS, while correlation between PHS resistance measurements was moderate. The heritability of PHS resistance was moderate and higher than grain yield. Significant quantitative trait loci with small effect were detected on chromosomes 1A, 1B, 5B, 7A and 7B. Both parents contributed to the PHS resistance. Promising DH genotypes with high and stable grain yield as well as PHS resistance were identified, suggesting that grain yield and PHS can be improved simultaneously in elite genetic materials, and that these DH genotypes will be useful parental material for durum breeding programs.
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Affiliation(s)
- A. K. Singh
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
- Present Address: Department of Agronomy, Iowa State University, Ames, IA USA
| | - R. E. Knox
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
| | - J. M. Clarke
- University of Saskatchewan, Saskatoon, SK Canada
| | - F. R. Clarke
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
| | - A. Singh
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
- Present Address: Department of Agronomy, Iowa State University, Ames, IA USA
| | - R. M. DePauw
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
| | - R. D. Cuthbert
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
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Kulwal P, Ishikawa G, Benscher D, Feng Z, Yu LX, Jadhav A, Mehetre S, Sorrells ME. Association mapping for pre-harvest sprouting resistance in white winter wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:793-805. [PMID: 22547141 DOI: 10.1007/s00122-012-1872-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Accepted: 04/04/2012] [Indexed: 05/06/2023]
Abstract
Association mapping identified quantitative trait loci (QTLs) and the markers linked to pre-harvest sprouting (PHS) resistance in an elite association mapping panel of white winter wheat comprising 198 genotypes. A total of 1,166 marker loci including DArT and SSR markers representing all 21 chromosomes of wheat were used in the analysis. General and mixed linear models were used to analyze PHS data collected over 4 years. Association analysis identified eight QTLs linked with 13 markers mapped on seven chromosomes. A QTL was detected on each arm of chromosome 2B and one each on chromosome arms 1BS, 2DS, 4AL, 6DL, 7BS and 7DS. All except the QTL on 7BS are located in a location similar to previous reports and, if verified, the QTL on 7BS is likely to be novel. Principal components and the kinship matrix were used to account for the presence of population structure but had only a minor effect on the results. Although, none of the QTLs was highly significant across all environments, a QTL on the long arm of chromosome 4A was detected in three different environments and also using the best linear unbiased predictions over years. Although previous reports have identified this as a major QTL, its effects were minor in our biparental mapping populations. The results of this study highlight the benefits of association mapping and the value of using elite material in association mapping for plant breeding programs.
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Affiliation(s)
- Pawan Kulwal
- State Level Biotechnology Centre, Mahatma Phule Agricultural University, Rahuri, 413 722 MS, India
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38
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A maize viviparous 1 gene increases seed dormancy and preharvest sprouting tolerance in transgenic wheat. J Cereal Sci 2012. [DOI: 10.1016/j.jcs.2011.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Liu S, Bai G. Dissection and fine mapping of a major QTL for preharvest sprouting resistance in white wheat Rio Blanco. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1395-404. [PMID: 20607209 DOI: 10.1007/s00122-010-1396-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 06/17/2010] [Indexed: 05/04/2023]
Abstract
Preharvest sprouting (PHS) is a major constraint to white wheat production. Previously, we mapped quantitative trait loci (QTL) for PHS resistance in white wheat by using a recombinant inbred line (RIL) population derived from the cross Rio Blanco/NW97S186. One QTL, QPhs.pseru-3A, showed a major effect on PHS resistance, and three simple sequence repeat (SSR) markers were mapped in the QTL region. To determine the flanking markers for the QTL and narrow down the QTL to a smaller chromosome region, we developed a new fine mapping population of 1,874 secondary segregating F(2) plants by selfing an F6 RIL (RIL25) that was heterozygous in the three SSR marker loci. Segregation of PHS resistance in the population fitted monogenic inheritance. An additive effect of the QTL played a major role on PHS resistance, but a dominant effect was also observed. Fifty-six recombinants among the three SSR markers were identified in the population and selfed to produce homozygous recombinants or QTL near-isogenic lines (NIL). PHS evaluation of the recombinants delineated the QTL in the region close to Xbarc57 flanked by Xbarc321 and Xbarc12. To saturate the QTL region, 11 amplified fragment length polymorphism (AFLP) markers were mapped in the QTL region with 7 AFLP co-segregated with Xbarc57 by using the NIL population. Dissection of the QTL as a Mendelian factor and saturation of the QTL region with additional markers created a solid foundation for positional cloning of the major QTL.
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Affiliation(s)
- Shubing Liu
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
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Kobayashi F, Takumi S, Handa H. Identification of quantitative trait loci for ABA responsiveness at the seedling stage associated with ABA-regulated gene expression in common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:629-41. [PMID: 20401645 DOI: 10.1007/s00122-010-1335-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 04/01/2010] [Indexed: 05/22/2023]
Abstract
Responsiveness to abscisic acid (ABA) during vegetative growth plays an important role in regulating adaptive responses to various environmental conditions, including activation of a number of ABA-responsive genes. However, the relationship between gene expression and responsiveness to ABA at the seedling stage has not been well studied in wheat. In the present study, quantitative trait locus (QTL) analysis for ABA responsiveness at the seedling stage was performed using recombinant inbred lines derived from a cross between common wheat cultivars showing different ABA responsiveness. Five QTLs were found to be significant, located on chromosomes 1B, 2A, 3A, 6D and 7B. The QTL with the greatest effect was located on chromosome 6D and explained 11.12% of the variance in ABA responsiveness. The other QTLs each accounted for approximately 5-8% of the phenotypic variation. Expression analyses of three ABA-responsive Cor/Lea genes, Wdhn13, Wrab15 and Wrab17, showed that allelic differences in QTLs on chromosomes 2A, 6D and 7B influenced expression of these genes in seedlings treated with ABA. The 3A QTL appeared to be involved in the regulatory system of Wdhn13 and Wrab15, but not Wrab17. The effects of the 2A and 6D QTLs on gene expression were relatively large. The combination of alleles at the QTLs resulted in an additive or synergistic effect on Cor/Lea expression. These results indicate that the QTLs influencing ABA responsiveness are associated with ABA-regulated gene expression and suggest that the QTL on chromosome 6D with the largest effect acts as a key regulator of ABA responses including seedling growth arrest and gene expression during the vegetative stage.
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Affiliation(s)
- Fuminori Kobayashi
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
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Gerjets T, Scholefield D, Foulkes MJ, Lenton JR, Holdsworth MJ. An analysis of dormancy, ABA responsiveness, after-ripening and pre-harvest sprouting in hexaploid wheat (Triticum aestivum L.) caryopses. JOURNAL OF EXPERIMENTAL BOTANY 2009; 61:597-607. [PMID: 19923197 PMCID: PMC2803222 DOI: 10.1093/jxb/erp329] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 10/21/2009] [Accepted: 10/22/2009] [Indexed: 05/19/2023]
Abstract
Embryo and caryopsis dormancy, abscisic acid (ABA) responsiveness, after-ripening (AR), and the disorder pre-harvest sprouting (PHS) were investigated in six genetically related wheat varieties previously characterized as resistant, intermediate, or susceptible to PHS. Timing of caryopsis AR differed between varieties; AR occurred before harvest ripeness in the most PHS-susceptible, whereas AR was slowest in the most PHS-resistant. Whole caryopses of all varieties showed little ABA-responsiveness during AR; PHS-susceptible varieties were responsive at the beginning of the AR period whereas PHS-resistant showed some responsiveness throughout. Isolated embryos showed relatively little dormancy during grain-filling and most varieties exhibited a window of decreased ABA-responsiveness around the period of maximum dry matter accumulation (physiological maturity). Susceptibility to PHS was assessed by overhead misting of either isolated ears or whole plants during AR; varieties were clearly distinguished using both methods. These analyses allowed an investigation of the interactions between the different components of seed development, compartments, and environment for the six varieties. There was no direct relationship between speed of caryopsis AR and embryo dormancy or ABA-responsiveness during seed maturation. However, the velocity of AR of a variety was closely associated with the degree of susceptibility to PHS during AR suggesting that these characters are developmentally linked. Investigation of genetic components of AR may therefore aid breeding approaches to reduce susceptibility to PHS.
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Affiliation(s)
- Tanja Gerjets
- Division of Plant and Crop Sciences, School of BioSciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Duncan Scholefield
- Division of Plant and Crop Sciences, School of BioSciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - M. John Foulkes
- Division of Plant and Crop Sciences, School of BioSciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - John R. Lenton
- Plant Science Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Michael J. Holdsworth
- Division of Plant and Crop Sciences, School of BioSciences, University of Nottingham, Nottingham LE12 5RD, UK
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Munkvold JD, Tanaka J, Benscher D, Sorrells ME. Mapping quantitative trait loci for preharvest sprouting resistance in white wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1223-35. [PMID: 19669633 DOI: 10.1007/s00122-009-1123-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 07/21/2009] [Indexed: 05/19/2023]
Abstract
The premature germination of seeds before harvest, known as preharvest sprouting (PHS), is a serious problem in all wheat growing regions of the world. In order to determine genetic control of PHS resistance in white wheat from the relatively uncharacterized North American germplasm, a doubled haploid population consisting of 209 lines from a cross between the PHS resistant variety Cayuga and the PHS susceptible variety Caledonia was used for QTL mapping. A total of 16 environments were used to detect 15 different PHS QTL including a major QTL, QPhs.cnl-2B.1, that was significant in all environments tested and explained from 5 to 31% of the trait variation in a given environment. Three other QTL QPhs.cnl-2D.1, QPhs.cnl-3D.1, and QPhs.cnl-6D.1 were detected in six, four, and ten environments, respectively. The potentially related traits of heading date (HD), plant height (HT), seed dormancy (DOR), and rate of germination (ROG) were also recorded in a limited number of environments. HD was found to be significantly negatively correlated with PHS score in most environments, likely due to a major HD QTL, QHd.cnl-2B.1, found to be tightly linked to the PHS QTL QPhs.cnl-2B.1. Using greenhouse grown material no overlap was found between seed dormancy and the four most consistent PHS QTL, suggesting that greenhouse environments are not representative of field environments. This study provides valuable information for marker-assisted breeding for PHS resistance, future haplotyping studies, and research into seed dormancy.
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Affiliation(s)
- Jesse D Munkvold
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA
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Characterization of polymorphic microsatellite loci in cultivated and wildPanax ginseng. Genes Genomics 2009. [DOI: 10.1007/bf03191145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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